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annotate coreograph.xml @ 0:99308601eaa6 draft

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"planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
author perssond
date Wed, 19 May 2021 21:34:38 +0000
parents
children 57f1260ca94e
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99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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1 <tool id="unet_coreograph" name="UNetCoreograph" version="@VERSION@.3" profile="17.09">
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2 <description>Coreograph uses UNet, a deep learning model, to identify complete/incomplete tissue cores on a tissue microarray. It has been trained on 9 TMA slides of different sizes and tissue types.</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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7 <expand macro="requirements"/>
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8 @VERSION_CMD@
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10 <command detect_errors="exit_code"><![CDATA[
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11 #set $type_corrected = str($source_image)[:-3]+'ome.tif'
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12 ln -s $source_image `basename $type_corrected`;
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14 @CMD_BEGIN@
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15 --imagePath `basename $type_corrected`
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16 --downsampleFactor $downsamplefactor
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17 --channel $channel
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18 --buffer $buffer
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19 --sensitivity $sensitivity
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21 ##if $usegrid
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22 ##--useGrid
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23 ##end if
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25 #if $cluster
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26 --cluster
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27 #end if
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29 --outputPath .;
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31 ]]></command>
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34 <inputs>
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35 <param name="source_image" type="data" format="tiff" label="Registered TIFF"/>
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36 <param name="downsamplefactor" type="integer" value="5" label="Down Sample Factor"/>
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37 <param name="channel" type="integer" value="0" label="Channel"/>
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38 <param name="buffer" type="float" value="2.0" label="Buffer"/>
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39 <param name="sensitivity" type="float" value="0.3" label="Sensitivity"/>
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40 <!--<param name="usegrid" type="boolean" label="Use Grid"/>-->
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41 <param name="cluster" type="boolean" checked="false" label="Cluster"/>
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42 </inputs>
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43
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44 <outputs>
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45 <collection name="tma_sections" type="list" label="${tool.name} on ${on_string}: Images">
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46 <discover_datasets pattern="(?P&lt;designation&gt;[0-9]+)\.tif" format="tiff" visible="false"/>
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47 </collection>
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48 <collection name="masks" type="list" label="${tool.name} on ${on_string}: Masks">
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49 <discover_datasets pattern="(?P&lt;designation&gt;[0-9]+)_mask\.tif" directory="masks" format="tiff" visible="false"/>
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50 </collection>
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51 <data name="TMA_MAP" format="tiff" label="${tool.name} on ${on_string}: TMA Map" from_work_dir="TMA_MAP.tif"/>
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52 </outputs>
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53 <help><![CDATA[
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54 ]]></help>
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55 <expand macro="citations" />
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56 </tool>